{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000864","ANALYSIS_ID":"AN001389","VERSION":"1","CREATED_ON":"August 11, 2017, 12:56 pm"},

"PROJECT":{"PROJECT_TITLE":"Mayo Pilot and Feasiblity: Targeting Myelin Metabolism of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI","PROJECT_SUMMARY":"CNS trauma generates a proteolytic imbalance contributing to secondary injury, including axonopathy and neuron degeneration. Kallikrein 6 (Klk6) is a serine protease implicated in neurodegeneration and here we investigate the role of protease activated receptors 1 (PAR1) and PAR2 in mediating these effects in mice with spinal cord injury (SCI). This project conducts untargeted Profiling (unbiased metabolomics assay) and targeted lipid analysis. The lipid assays are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin.","INSTITUTE":"Mayo Clinic","LAST_NAME":"Scarisbrick","FIRST_NAME":"Isobel","ADDRESS":"200 First Street SW, Rochester, MN 55905","EMAIL":"scarisbrick.isobel@mayo.edu","PHONE":"507-284-0124"},

"STUDY":{"STUDY_TITLE":"Targeting Myelin Ceramides in PAR1 and PAR2 Mice after SCI","STUDY_SUMMARY":"Targeting Myelin ceramides in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.","INSTITUTE":"Mayo Clinic","LAST_NAME":"Scarisbrick","FIRST_NAME":"Isobel","ADDRESS":"200 First Street SW, Rochester, MN 55905","EMAIL":"scarisbrick.isobel@mayo.edu","PHONE":"507-284-0124"},

"SUBJECT":{"SUBJECT_TYPE":"Mouse","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ms6121-1",
"Factors":{"timept":"P60","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-2",
"Factors":{"timept":"P60","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-3",
"Factors":{"timept":"P60","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-10",
"Factors":{"timept":"P60","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-11",
"Factors":{"timept":"P60","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-4",
"Factors":{"timept":"P60","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-5",
"Factors":{"timept":"P60","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-6",
"Factors":{"timept":"P60","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-12",
"Factors":{"timept":"P60","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-13",
"Factors":{"timept":"P60","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-7",
"Factors":{"timept":"P60","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-8",
"Factors":{"timept":"P60","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-9",
"Factors":{"timept":"P60","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-14",
"Factors":{"timept":"P60","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-15",
"Factors":{"timept":"P60","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-16",
"Factors":{"timept":"P21","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-17",
"Factors":{"timept":"P21","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-18",
"Factors":{"timept":"P21","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-19",
"Factors":{"timept":"P21","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-20",
"Factors":{"timept":"P21","Grouping":"CTRL"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-21",
"Factors":{"timept":"P21","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-22",
"Factors":{"timept":"P21","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-23",
"Factors":{"timept":"P21","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-24",
"Factors":{"timept":"P21","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-25",
"Factors":{"timept":"P21","Grouping":"PAR1"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-26",
"Factors":{"timept":"P21","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-27",
"Factors":{"timept":"P21","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-28",
"Factors":{"timept":"P21","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-29",
"Factors":{"timept":"P21","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
},
{
"Subject ID":"-",
"Sample ID":"ms6121-30",
"Factors":{"timept":"P21","Grouping":"PAR2"},
"Additional sample data":{"gender":"female","Sample type":"spinal cord","Species":"mouse"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"This prior project involved frozen whole mouse spinal cord (SC) samples for Untargeted Profiling (unbiased metabolomics assay). There were 9 samples total, n=3 for each genotype that includes wild type control, PAR1 KO and PAR2 KO at P60 days. Your team prepared the samples and ran the profiling and provided us with the results. Since the outcome of this preliminary study using 3 animals for each genotype looked so promising, we discussed bringing the total number to 5 and re-running to improve the power. Therefore, we are submitting 2 more samples for each genotype at P60. In addition, we are providing 5 samples for each genotype at P21 (an earlier age) for additional comparisons. To bring n=5 for each P60 genotype we provide 2 more samples per genotype. In addition we provide n=5 for P21 for each genotype (wild type, PAR1 and PAR2)."},

"TREATMENT":{"TREATMENT_SUMMARY":"A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"ceramides of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C8 (150 x 2mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Quantum Ultra","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"units = ng/vial",

"Data":[{"Metabolite":"Sph","ms6121-1":"1.59","ms6121-2":"2.55","ms6121-3":"1.90","ms6121-10":"3.34","ms6121-11":"3.89","ms6121-4":"2.59","ms6121-5":"2.29","ms6121-6":"3.08","ms6121-12":"2.95","ms6121-13":"2.35","ms6121-7":"1.85","ms6121-8":"2.43","ms6121-9":"2.09","ms6121-14":"2.64","ms6121-15":"2.21","ms6121-18":"1.22","ms6121-19":"1.53","ms6121-21":"2.41","ms6121-22":"1.91","ms6121-23":"1.51","ms6121-24":"1.34","ms6121-25":"2.01","ms6121-26":"1.50","ms6121-27":"1.60","ms6121-28":"0.92","ms6121-29":"1.47","ms6121-30":"1.73"},{"Metabolite":"SPA","ms6121-1":"0.41","ms6121-2":"0.60","ms6121-3":"0.39","ms6121-10":"0.62","ms6121-11":"0.64","ms6121-4":"0.60","ms6121-5":"0.49","ms6121-6":"0.60","ms6121-12":"0.65","ms6121-13":"0.52","ms6121-7":"0.47","ms6121-8":"0.47","ms6121-9":"0.47","ms6121-14":"0.51","ms6121-15":"0.45","ms6121-18":"0.61","ms6121-19":"0.72","ms6121-21":"0.88","ms6121-22":"0.75","ms6121-23":"0.73","ms6121-24":"0.68","ms6121-25":"0.96","ms6121-26":"0.71","ms6121-27":"0.61","ms6121-28":"0.42","ms6121-29":"0.71","ms6121-30":"0.79"},{"Metabolite":"S1P","ms6121-1":"5.33","ms6121-2":"8.95","ms6121-3":"7.05","ms6121-10":"13.30","ms6121-11":"16.98","ms6121-4":"13.53","ms6121-5":"10.97","ms6121-6":"12.62","ms6121-12":"10.46","ms6121-13":"9.82","ms6121-7":"7.00","ms6121-8":"11.90","ms6121-9":"10.07","ms6121-14":"12.86","ms6121-15":"9.76","ms6121-18":"2.30","ms6121-19":"4.20","ms6121-21":"5.40","ms6121-22":"6.18","ms6121-23":"5.03","ms6121-24":"3.05","ms6121-25":"6.95","ms6121-26":"3.83","ms6121-27":"3.78","ms6121-28":"1.36","ms6121-29":"2.90","ms6121-30":"3.05"},{"Metabolite":"C8-cer","ms6121-1":"0.00","ms6121-2":"0.00","ms6121-3":"0.00","ms6121-10":"0.00","ms6121-11":"0.00","ms6121-4":"0.00","ms6121-5":"0.00","ms6121-6":"0.00","ms6121-12":"0.00","ms6121-13":"0.00","ms6121-7":"0.00","ms6121-8":"0.00","ms6121-9":"0.00","ms6121-14":"0.00","ms6121-15":"0.00","ms6121-18":"0.00","ms6121-19":"0.00","ms6121-21":"0.00","ms6121-22":"0.00","ms6121-23":"0.00","ms6121-24":"0.00","ms6121-25":"0.00","ms6121-26":"0.00","ms6121-27":"0.00","ms6121-28":"0.00","ms6121-29":"0.00","ms6121-30":"0.00"},{"Metabolite":"C14-cer","ms6121-1":"0.05","ms6121-2":"0.13","ms6121-3":"0.05","ms6121-10":"0.15","ms6121-11":"0.47","ms6121-4":"0.16","ms6121-5":"0.08","ms6121-6":"0.24","ms6121-12":"0.25","ms6121-13":"0.07","ms6121-7":"0.11","ms6121-8":"0.09","ms6121-9":"0.12","ms6121-14":"0.08","ms6121-15":"0.22","ms6121-18":"0.20","ms6121-19":"0.22","ms6121-21":"0.71","ms6121-22":"0.80","ms6121-23":"0.35","ms6121-24":"0.23","ms6121-25":"0.51","ms6121-26":"0.26","ms6121-27":"0.29","ms6121-28":"0.08","ms6121-29":"0.09","ms6121-30":"0.26"},{"Metabolite":"C16-cer","ms6121-1":"2.71","ms6121-2":"3.56","ms6121-3":"2.20","ms6121-10":"4.68","ms6121-11":"5.45","ms6121-4":"2.73","ms6121-5":"1.88","ms6121-6":"4.91","ms6121-12":"3.04","ms6121-13":"2.19","ms6121-7":"2.08","ms6121-8":"1.70","ms6121-9":"1.55","ms6121-14":"1.89","ms6121-15":"1.71","ms6121-18":"1.21","ms6121-19":"1.96","ms6121-21":"3.62","ms6121-22":"2.55","ms6121-23":"1.82","ms6121-24":"1.56","ms6121-25":"2.41","ms6121-26":"1.57","ms6121-27":"1.77","ms6121-28":"0.65","ms6121-29":"1.11","ms6121-30":"1.60"},{"Metabolite":"C16-dh 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cer","ms6121-1":"2.82","ms6121-2":"2.86","ms6121-3":"2.53","ms6121-10":"2.59","ms6121-11":"2.15","ms6121-4":"2.38","ms6121-5":"3.04","ms6121-6":"2.53","ms6121-12":"2.35","ms6121-13":"2.33","ms6121-7":"2.07","ms6121-8":"2.97","ms6121-9":"2.95","ms6121-14":"3.69","ms6121-15":"1.97","ms6121-18":"8.64","ms6121-19":"8.27","ms6121-21":"7.72","ms6121-22":"10.41","ms6121-23":"11.90","ms6121-24":"11.05","ms6121-25":"12.83","ms6121-26":"10.57","ms6121-27":"6.70","ms6121-28":"5.40","ms6121-29":"7.08","ms6121-30":"7.82"},{"Metabolite":"C20-cer","ms6121-1":"28.78","ms6121-2":"38.28","ms6121-3":"33.47","ms6121-10":"41.44","ms6121-11":"46.79","ms6121-4":"34.27","ms6121-5":"34.03","ms6121-6":"57.87","ms6121-12":"44.85","ms6121-13":"30.86","ms6121-7":"20.36","ms6121-8":"42.70","ms6121-9":"29.85","ms6121-14":"51.43","ms6121-15":"32.91","ms6121-18":"31.23","ms6121-19":"38.88","ms6121-21":"50.07","ms6121-22":"55.20","ms6121-23":"58.65","ms6121-24":"46.29","ms6121-25":"63.13","ms6121-26":"49.05","ms6121-27":"42.21","ms6121-28":"17.81","ms6121-29":"30.71","ms6121-30":"43.27"},{"Metabolite":"C22-cer","ms6121-1":"53.32","ms6121-2":"78.00","ms6121-3":"59.52","ms6121-10":"90.13","ms6121-11":"127.08","ms6121-4":"87.60","ms6121-5":"65.85","ms6121-6":"104.85","ms6121-12":"89.76","ms6121-13":"81.31","ms6121-7":"43.47","ms6121-8":"75.75","ms6121-9":"71.00","ms6121-14":"115.42","ms6121-15":"89.20","ms6121-18":"45.35","ms6121-19":"49.72","ms6121-21":"107.85","ms6121-22":"105.62","ms6121-23":"73.38","ms6121-24":"58.35","ms6121-25":"85.16","ms6121-26":"77.57","ms6121-27":"86.19","ms6121-28":"30.98","ms6121-29":"49.36","ms6121-30":"73.68"},{"Metabolite":"C24:1-cer","ms6121-1":"134.04","ms6121-2":"147.96","ms6121-3":"135.10","ms6121-10":"137.58","ms6121-11":"142.73","ms6121-4":"151.71","ms6121-5":"142.94","ms6121-6":"185.11","ms6121-12":"128.65","ms6121-13":"130.02","ms6121-7":"112.42","ms6121-8":"128.34","ms6121-9":"134.91","ms6121-14":"132.52","ms6121-15":"125.44","ms6121-18":"109.96","ms6121-19":"103.41","ms6121-21":"142.85","ms6121-22":"142.37","ms6121-23":"114.49","ms6121-24":"111.28","ms6121-25":"127.48","ms6121-26":"112.09","ms6121-27":"112.25","ms6121-28":"81.04","ms6121-29":"94.86","ms6121-30":"105.13"},{"Metabolite":"C24-cer","ms6121-1":"23.84","ms6121-2":"29.29","ms6121-3":"24.04","ms6121-10":"29.91","ms6121-11":"41.51","ms6121-4":"28.36","ms6121-5":"25.57","ms6121-6":"30.30","ms6121-12":"32.26","ms6121-13":"29.27","ms6121-7":"15.90","ms6121-8":"24.18","ms6121-9":"24.85","ms6121-14":"36.39","ms6121-15":"31.46","ms6121-18":"24.70","ms6121-19":"25.44","ms6121-21":"40.99","ms6121-22":"36.54","ms6121-23":"29.46","ms6121-24":"26.60","ms6121-25":"31.36","ms6121-26":"32.62","ms6121-27":"37.50","ms6121-28":"20.46","ms6121-29":"25.68","ms6121-30":"34.37"}],

"Metabolites":[{"metabolite_name":"Sph"},{"metabolite_name":"SPA"},{"metabolite_name":"S1P"},{"metabolite_name":"C8-cer"},{"metabolite_name":"C14-cer"},{"metabolite_name":"C16-cer"},{"metabolite_name":"C16-dh cer"},{"metabolite_name":"C18:1-cer"},{"metabolite_name":"C18:1-dh cer"},{"metabolite_name":"C18-cer"},{"metabolite_name":"C18-dh cer"},{"metabolite_name":"C20-cer"},{"metabolite_name":"C22-cer"},{"metabolite_name":"C24:1-cer"},{"metabolite_name":"C24-cer"}]
}

}